"There's no telling what goes on below the Planck Limit. " But the electron is quite big compared to the Plack limit: about 1000000000000000 times bigger. That's without quantum effects spreading it out and making it even bigger.

"when a photon a million light-years away hits your eye, to the photon, no time has passed, " For the photon, as you said. But for us, up to a couple of million years ago (if the photon came from the Andromeda galaxy). The photon's timelessness has been invoked as an explanation of two slit experiments (by Gribbin or Gould, I can't remember which), because the photon has all the time in the world to try all possible paths. Perhaps there's only one ohoton in the Universe, being everywhere at once?

But that doesn't cover the same experiment carried out with electrons, atoms, molecules (even surprisingly big ones - I'm told Schroedinger repeated the experiment with cats).

"Our equations fall apart": they do an' all. Maths is an approximation to reality. There are no infinite straight lines, perfect circles, dimensionless points*, or right angles in reality. Plato thought this meant that the imperfect world is not true, whereas the ideal mathematical one is. I think it's the other way about, but them I'm an engineer, and used to finding that my bright idea stretched the model too far. Quantum maths is an approximation. It has to be, it tells us nothing about gravity and it's struggling with the mass/ energy content of the Universe.

"There may be an infinitesimally tiny universe down there". Probably exactly ours, not a clone exactly the same. The Universe was created by Maurice Escher.